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function 'as_cholmod_sparse' not provided by package 'Matrix' #1599

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realmungmung opened this issue Jan 19, 2024 · 6 comments
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function 'as_cholmod_sparse' not provided by package 'Matrix' #1599

realmungmung opened this issue Jan 19, 2024 · 6 comments
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@realmungmung
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Following the PBMC signac intruction, got this error when running pbmc <- RunSVD(pbmc):

Error in irlba(A = t(x = object), nv = n, work = irlba.work, tol = tol) :
function 'as_cholmod_sparse' not provided by package 'Matrix'

Tried the solution:
install.packages("irlba", type="source")
install.packages("Matrix", type = "source")
install.packages("SeuratObject", type = "source")

But still got the same error after reopen the Rstudio again
@realmungmung realmungmung added the bug Something isn't working label Jan 19, 2024
@realmungmung
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also after I installed the packages in R, it showed that Matrix and irlba are not installed when I opened Rstudio

@realmungmung
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realmungmung commented Jan 19, 2024 •
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after installation in R, it also showed in the R console:
1: In install.packages("SeuratObject", type = "source") :
installation of package ‘Matrix’ had non-zero exit status
2: In install.packages("SeuratObject", type = "source") :
installation of package ‘SeuratObject’ had non-zero exit status
In install.packages("irlba", type = "source") :
installation of package ‘irlba’ had non-zero exit status

@realmungmung
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─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.3.2 (2023-10-31)
os macOS Sonoma 14.2.1
system aarch64, darwin20
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/Los_Angeles
date 2024-01-19
rstudio 2023.12.0+369 Ocean Storm (desktop)
pandoc 3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 4.3.0)
AnnotationDbi * 1.64.1 2023-11-02 [1] Bioconductor
AnnotationFilter * 1.26.0 2023-10-26 [1] Bioconductor
backports 1.4.1 2021-12-13 [1] CRAN (R 4.3.0)
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.3.0)
Biobase * 2.62.0 2023-10-26 [1] Bioconductor
BiocFileCache 2.10.1 2023-10-26 [1] Bioconductor
BiocGenerics * 0.48.1 2023-11-02 [1] Bioconductor
BiocIO 1.12.0 2023-10-26 [1] Bioconductor
BiocParallel 1.36.0 2023-10-26 [1] Bioconductor
biomaRt 2.58.0 2023-10-26 [1] Bioconductor
Biostrings 2.70.1 2023-10-26 [1] Bioconductor
biovizBase * 1.50.0 2023-10-26 [1] Bioconductor
bit 4.0.5 2022-11-15 [1] CRAN (R 4.3.0)
bit64 4.0.5 2020-08-30 [1] CRAN (R 4.3.0)
bitops 1.0-7 2021-04-24 [1] CRAN (R 4.3.0)
blob 1.2.4 2023-03-17 [1] CRAN (R 4.3.0)
BSgenome 1.70.1 2023-11-02 [1] Bioconductor
cachem 1.0.8 2023-05-01 [1] CRAN (R 4.3.0)
checkmate 2.3.1 2023-12-04 [1] CRAN (R 4.3.1)
cli 3.6.2 2023-12-11 [1] CRAN (R 4.3.1)
cluster 2.1.6 2023-12-01 [1] CRAN (R 4.3.1)
codetools 0.2-19 2023-02-01 [1] CRAN (R 4.3.2)
colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.3.0)
cowplot 1.1.2 2023-12-15 [1] CRAN (R 4.3.1)
crayon 1.5.2 2022-09-29 [1] CRAN (R 4.3.0)
curl 5.2.0 2023-12-08 [1] CRAN (R 4.3.1)
data.table 1.14.10 2023-12-08 [1] CRAN (R 4.3.1)
DBI 1.2.1 2024-01-12 [1] CRAN (R 4.3.2)
dbplyr 2.4.0 2023-10-26 [1] CRAN (R 4.3.1)
DelayedArray 0.28.0 2023-11-06 [1] Bioconductor
deldir 2.0-2 2023-11-23 [1] CRAN (R 4.3.1)
dichromat 2.0-0.1 2022-05-02 [1] CRAN (R 4.3.0)
digest 0.6.34 2024-01-11 [1] CRAN (R 4.3.1)
dotCall64 1.1-1 2023-11-28 [1] CRAN (R 4.3.1)
dplyr * 1.1.4 2023-11-17 [1] CRAN (R 4.3.1)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.3.0)
EnsDb.Hsapiens.v75 * 2.99.0 2024-01-16 [1] Bioconductor
ensembldb * 2.26.0 2023-10-26 [1] Bioconductor
evaluate 0.23 2023-11-01 [1] CRAN (R 4.3.1)
fansi 1.0.6 2023-12-08 [1] CRAN (R 4.3.1)
farver 2.1.1 2022-07-06 [1] CRAN (R 4.3.0)
fastDummies 1.7.3 2023-07-06 [1] CRAN (R 4.3.0)
fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0)
fastmatch 1.1-4 2023-08-18 [1] CRAN (R 4.3.0)
filelock 1.0.3 2023-12-11 [1] CRAN (R 4.3.1)
fitdistrplus 1.1-11 2023-04-25 [1] CRAN (R 4.3.0)
foreign 0.8-86 2023-11-28 [1] CRAN (R 4.3.1)
Formula 1.2-5 2023-02-24 [1] CRAN (R 4.3.0)
future 1.33.1 2023-12-22 [1] CRAN (R 4.3.1)
future.apply 1.11.1 2023-12-21 [1] CRAN (R 4.3.1)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0)
GenomeInfoDb * 1.38.5 2023-12-30 [1] Bioconductor 3.18 (R 4.3.2)
GenomeInfoDbData 1.2.11 2024-01-12 [1] Bioconductor
GenomicAlignments 1.38.1 2024-01-13 [1] Bioconductor 3.18 (R 4.3.2)
GenomicFeatures * 1.54.1 2023-10-30 [1] Bioconductor
GenomicRanges * 1.54.1 2023-10-30 [1] Bioconductor
ggplot2 * 3.4.4 2023-10-12 [1] CRAN (R 4.3.1)
ggrepel 0.9.5 2024-01-10 [1] CRAN (R 4.3.1)
ggridges 0.5.5 2023-12-15 [1] CRAN (R 4.3.1)
globals 0.16.2 2022-11-21 [1] CRAN (R 4.3.0)
glue 1.7.0 2024-01-09 [1] CRAN (R 4.3.1)
goftest 1.2-3 2021-10-07 [1] CRAN (R 4.3.0)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.3.0)
gtable 0.3.4 2023-08-21 [1] CRAN (R 4.3.0)
hdf5r * 1.3.9 2024-01-14 [1] CRAN (R 4.3.1)
Hmisc 5.1-1 2023-09-12 [1] CRAN (R 4.3.0)
hms 1.1.3 2023-03-21 [1] CRAN (R 4.3.0)
htmlTable 2.4.2 2023-10-29 [1] CRAN (R 4.3.1)
htmltools 0.5.7 2023-11-03 [1] CRAN (R 4.3.1)
htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.3.1)
httpuv 1.6.13 2023-12-06 [1] CRAN (R 4.3.1)
httr 1.4.7 2023-08-15 [1] CRAN (R 4.3.0)
ica 1.0-3 2022-07-08 [1] CRAN (R 4.3.0)
igraph 1.6.0 2023-12-11 [1] CRAN (R 4.3.1)
IRanges * 2.36.0 2023-10-26 [1] Bioconductor
irlba * 2.3.5.1 2022-10-03 [1] CRAN (R 4.3.0)
jsonlite 1.8.8 2023-12-04 [1] CRAN (R 4.3.1)
KEGGREST 1.42.0 2023-10-26 [1] Bioconductor
KernSmooth 2.23-22 2023-07-10 [1] CRAN (R 4.3.2)
knitr 1.45 2023-10-30 [1] CRAN (R 4.3.1)
labeling 0.4.3 2023-08-29 [1] CRAN (R 4.3.0)
later 1.3.2 2023-12-06 [1] CRAN (R 4.3.1)
lattice 0.22-5 2023-10-24 [1] CRAN (R 4.3.1)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.3.0)
leiden 0.4.3.1 2023-11-17 [1] CRAN (R 4.3.1)
lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.3.1)
listenv 0.9.0 2022-12-16 [1] CRAN (R 4.3.0)
lmtest 0.9-40 2022-03-21 [1] CRAN (R 4.3.0)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0)
MASS 7.3-60.0.1 2024-01-13 [1] CRAN (R 4.3.1)
Matrix * 1.6-5 2024-01-11 [1] CRAN (R 4.3.1)
MatrixGenerics 1.14.0 2023-10-26 [1] Bioconductor
matrixStats 1.2.0 2023-12-11 [1] CRAN (R 4.3.1)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.0)
mime 0.12 2021-09-28 [1] CRAN (R 4.3.0)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.3.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.3.0)
nlme 3.1-164 2023-11-27 [1] CRAN (R 4.3.1)
nnet 7.3-19 2023-05-03 [1] CRAN (R 4.3.2)
parallelly 1.36.0 2023-05-26 [1] CRAN (R 4.3.0)
patchwork * 1.2.0 2024-01-08 [1] CRAN (R 4.3.1)
pbapply 1.7-2 2023-06-27 [1] CRAN (R 4.3.0)
pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0)
plotly 4.10.4 2024-01-13 [1] CRAN (R 4.3.1)
plyr 1.8.9 2023-10-02 [1] CRAN (R 4.3.1)
png 0.1-8 2022-11-29 [1] CRAN (R 4.3.0)
polyclip 1.10-6 2023-09-27 [1] CRAN (R 4.3.1)
prettyunits 1.2.0 2023-09-24 [1] CRAN (R 4.3.1)
progress 1.2.3 2023-12-06 [1] CRAN (R 4.3.1)
progressr 0.14.0 2023-08-10 [1] CRAN (R 4.3.0)
promises 1.2.1 2023-08-10 [1] CRAN (R 4.3.0)
ProtGenerics 1.34.0 2023-10-26 [1] Bioconductor
purrr 1.0.2 2023-08-10 [1] CRAN (R 4.3.0)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0)
RANN 2.6.1 2019-01-08 [1] CRAN (R 4.3.0)
rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.3.0)
RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.3.0)
Rcpp 1.0.12 2024-01-09 [1] CRAN (R 4.3.1)
RcppAnnoy 0.0.21 2023-07-02 [1] CRAN (R 4.3.0)
RcppHNSW 0.5.0 2023-09-19 [1] CRAN (R 4.3.1)
RcppRoll 0.3.0 2018-06-05 [1] CRAN (R 4.3.0)
RCurl 1.98-1.14 2024-01-09 [1] CRAN (R 4.3.1)
reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.3.0)
restfulr 0.0.15 2022-06-16 [1] CRAN (R 4.3.0)
reticulate 1.34.0 2023-10-12 [1] CRAN (R 4.3.1)
rjson 0.2.21 2022-01-09 [1] CRAN (R 4.3.0)
rlang 1.1.3 2024-01-10 [1] CRAN (R 4.3.1)
rmarkdown 2.25 2023-09-18 [1] CRAN (R 4.3.1)
ROCR 1.0-11 2020-05-02 [1] CRAN (R 4.3.0)
rpart 4.1.23 2023-12-05 [1] CRAN (R 4.3.1)
Rsamtools 2.18.0 2023-10-26 [1] Bioconductor
RSpectra 0.16-1 2022-04-24 [1] CRAN (R 4.3.0)
RSQLite 2.3.4 2023-12-08 [1] CRAN (R 4.3.1)
rstudioapi 0.15.0 2023-07-07 [1] CRAN (R 4.3.0)
rtracklayer 1.62.0 2023-10-26 [1] Bioconductor
Rtsne 0.17 2023-12-07 [1] CRAN (R 4.3.1)
S4Arrays 1.2.0 2023-10-26 [1] Bioconductor
S4Vectors * 0.40.2 2023-11-25 [1] Bioconductor 3.18 (R 4.3.2)
scales 1.3.0 2023-11-28 [1] CRAN (R 4.3.1)
scattermore 1.2 2023-06-12 [1] CRAN (R 4.3.0)
sctransform 0.4.1 2023-10-19 [1] CRAN (R 4.3.1)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.0)
Seurat * 5.0.1 2023-11-17 [1] CRAN (R 4.3.1)
SeuratObject * 5.0.1 2023-11-17 [1] CRAN (R 4.3.2)
shiny 1.8.0 2023-11-17 [1] CRAN (R 4.3.1)
Signac * 1.12.9004 2024-01-18 [1] Github (0c43d88)
sp * 2.1-2 2023-11-26 [1] CRAN (R 4.3.1)
spam 2.10-0 2023-10-23 [1] CRAN (R 4.3.1)
SparseArray 1.2.3 2023-12-26 [1] Bioconductor 3.18 (R 4.3.2)
spatstat.data * 3.0-4 2024-01-15 [1] CRAN (R 4.3.1)
spatstat.explore 3.2-5 2023-10-22 [1] CRAN (R 4.3.1)
spatstat.geom * 3.2-7 2023-10-20 [1] CRAN (R 4.3.1)
spatstat.random 3.2-2 2023-11-29 [1] CRAN (R 4.3.1)
spatstat.sparse 3.0-3 2023-10-24 [1] CRAN (R 4.3.1)
spatstat.utils 3.0-4 2023-10-24 [1] CRAN (R 4.3.1)
stringi 1.8.3 2023-12-11 [1] CRAN (R 4.3.1)
stringr 1.5.1 2023-11-14 [1] CRAN (R 4.3.1)
SummarizedExperiment 1.32.0 2023-11-06 [1] Bioconductor
survival 3.5-7 2023-08-14 [1] CRAN (R 4.3.2)
tensor 1.5 2012-05-05 [1] CRAN (R 4.3.0)
tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.0)
tidyr 1.3.0 2023-01-24 [1] CRAN (R 4.3.0)
tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.3.0)
utf8 1.2.4 2023-10-22 [1] CRAN (R 4.3.1)
uwot 0.1.16 2023-06-29 [1] CRAN (R 4.3.0)
VariantAnnotation 1.48.1 2023-11-18 [1] Bioconductor 3.18 (R 4.3.2)
vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.3.1)
viridisLite 0.4.2 2023-05-02 [1] CRAN (R 4.3.0)
withr 3.0.0 2024-01-16 [1] CRAN (R 4.3.1)
xfun 0.41 2023-11-01 [1] CRAN (R 4.3.1)
XML 3.99-0.16 2023-11-29 [1] CRAN (R 4.3.1)
xml2 1.3.6 2023-12-04 [1] CRAN (R 4.3.1)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.3.0)
XVector 0.42.0 2023-10-26 [1] Bioconductor
yaml 2.3.8 2023-12-11 [1] CRAN (R 4.3.1)
zlibbioc 1.48.0 2023-10-26 [1] Bioconductor
zoo 1.8-12 2023-04-13 [1] CRAN (R 4.3.0)

@timoast
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timoast commented Jan 22, 2024

Please see #1596

@timoast timoast closed this as completed Jan 22, 2024
@realmungmung
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downloaded GNU Fortran compiler from https://mac.r-project.org/tools/ to help installing irlba

@realmungmung
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Please see #1596

Thanks so much

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